But what should I do if my website has a multiple column layout where, for instance, one column shows the latest posts, and the other column lists the latest posts from a tag (highlights)? i.e. essentially there are two containers.

I tried these two snippets (see below), and either way, infinite scrolling is only enabled for one column/container.

You'll have to duplicate line 475 of '/modules/infinity-scroll/infinity.js' as this initializes infinite scroll. (Do you see the variable name match?)

infiniteScroll.scroller = new Scroller( infiniteScroll.settings );

What's more, you'll have to tweak the module to accept more attributes, or at least post_type attribute to be able to determine what post_type to bring for each inifinite loop -- this must be done in both JS and PHP (callback for ajax function).